The MAGPIE research group studies the dynamics of diverse interacting pathogens. We are building tools to use pathogen genomic data to help us understand transmission patterns. We develop novel approaches to analyze and compare phylogenetic trees. We develop and test ecological and epidemiological models.

We draw on tools from across mathematics and statistics, including ordinary differential equation models, stochastic “individual-based” models, branching processes, probability and optimization, Bayesian inference, Markov chain Monte Carlo sampling, and machine learning. Our researchers have diverse backgrounds, primarily in mathematics, but also in statistics, quantitative biology and computer science.We also support public health with pandemic modelling alongside our own research. Our work involves case forecasting, parameter estimation, understanding the impact of rapid testing and other measures, genomic epidemiology and other topics in COVID-19 and other respiratory infections.

We are situated in the mathematics department at SFU. To apply to join us as a graduate student, please see apply to the department, mentioning the MAGPIE group in your application. You do not need a formal biology background to join our group, but a curiosity and enthusiasm for research in our areas will be very helpful.

In The Media


A fast and scalable method for inferring phylogenetic networks from trees by aligning lineage taxon strings

MAY 2023

Louxin Zhang, Niloufar Niloufar Abhari, Caroline Colijn, Yufeng Wu

COVID-19 endgame: From pandemic to endemic? Vaccination, reopening and evolution in low-and high-vaccinated populations


Elisha B Are, Yexuan Song, Jessica E Stockdale, Paul Tupper, Caroline Colijn . Journal of Theoretical Biology.

Spatial modeling of M. tuberculosis transmission with dyadic genetic relatedness data


Joshua L Warren, Melanie H Chitwood, Benjamin Sobkowiak, Caroline Colijn, Ted Cohen. Biometrics.

A Fast and Scalable Method for Inferring Phylogenetic Networks from Trees by Aligning Lineage Taxon Strings

January 2023

Louxin Zhang, Niloufar Abhari, Caroline Colijn, Yufeng Wu. arXiv preprint arXiv:2301.00992.